Elsevier

Methods

Volume 115, 15 February 2017, Pages 80-90
Methods

TrackMate: An open and extensible platform for single-particle tracking

https://doi.org/10.1016/j.ymeth.2016.09.016Get rights and content
Under a Creative Commons license
open access

Highlights

  • TrackMate is a software tool for automated, and semi-automated particle tracking.

  • TrackMate’s major development focus is on usability and extensibility.

  • TrackMate leverages Fiji to help provides its functionality and extensibility.

  • TrackMate is used for: C. elegans lineaging, NEMO assembly and clathrin dynamics.

  • Challenging imaging problems can robustly be analyzed using semi-automatic methods.

Abstract

We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools.

The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.

Abbreviations

GUI
Graphical User Interface
LSCM
Laser Scanning Confocal Microscope
SDCM
Spinning-Disk Confocal Microscope
TIRFM
Total-Internal Reflection Fluorescence Microscope
VAEM
Variable Angle Epifluorescence Microscopy
QE
Quantum Efficiency

Keywords

Single-particle tracking
Phototoxicity
Clathin-mediated endocytosis
Image analysis
Open-source software
Microscopy

Cited by (0)

1

Present address: Palantir Technologies, USA.

2

Present address: Microsoft GmbH, Germany.